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| author | CoprDistGit <infra@openeuler.org> | 2023-05-05 03:29:13 +0000 |
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| committer | CoprDistGit <infra@openeuler.org> | 2023-05-05 03:29:13 +0000 |
| commit | 3e7504912f67b423678e3497f72c46d63e8c5423 (patch) | |
| tree | f375d3ff8b6f9d715a7ca3952ec46242857caba3 | |
| parent | 7291935f8038d784107985b2002b8570617d7b5a (diff) | |
automatic import of python-coupledmodeldriveropeneuler20.03
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-coupledmodeldriver.spec | 924 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 926 insertions, 0 deletions
@@ -0,0 +1 @@ +/coupledmodeldriver-1.6.5.tar.gz diff --git a/python-coupledmodeldriver.spec b/python-coupledmodeldriver.spec new file mode 100644 index 0000000..d678489 --- /dev/null +++ b/python-coupledmodeldriver.spec @@ -0,0 +1,924 @@ +%global _empty_manifest_terminate_build 0 +Name: python-coupledmodeldriver +Version: 1.6.5 +Release: 1 +Summary: coupled model configuration generation +License: CC0-1.0 +URL: https://github.com/noaa-ocs-modeling/CoupledModelDriver.git +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/43/6f/58efdd338579dffb5b12efc29f326288840574e6446d463b01079f1362a4/coupledmodeldriver-1.6.5.tar.gz +BuildArch: noarch + +Requires: python3-adcircpy +Requires: python3-file-read-backwards +Requires: python3-nemspy +Requires: python3-numpy +Requires: python3-pyproj +Requires: python3-typepigeon +Requires: python3-isort +Requires: python3-oitnb +Requires: python3-pooch +Requires: python3-pyschism +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-pytest-socket +Requires: python3-pytest-xdist +Requires: python3-m2r2 +Requires: python3-sphinx +Requires: python3-sphinx-rtd-theme +Requires: python3-sphinxcontrib-programoutput + +%description +# CoupledModelDriver + +[](https://github.com/noaa-ocs-modeling/CoupledModelDriver/actions?query=workflow%3Atests) +[](https://codecov.io/gh/noaa-ocs-modeling/coupledmodeldriver) +[](https://github.com/noaa-ocs-modeling/CoupledModelDriver/actions?query=workflow%3Abuild) +[](https://pypi.org/project/CoupledModelDriver) +[](https://creativecommons.org/share-your-work/public-domain/cc0) +[](https://sourceforge.net/p/oitnb/code) +[](https://coupledmodeldriver.readthedocs.io/en/latest/?badge=latest) + +CoupledModelDriver generates an overlying job submission framework and configuration directories for NEMS-coupled coastal ocean +model ensembles. + +```shell +pip install coupledmodeldriver +``` + +It utilizes [NEMSpy](https://nemspy.readthedocs.io) to generate NEMS configuration files, shares common configurations between +runs, and organizes spinup and mesh partition into separate jobs for dependant submission. + +Documentation can be found at https://coupledmodeldriver.readthedocs.io + +## supported models and platforms + +- **models** + - circulation models + - ADCIRC (uses [ADCIRCpy](https://pypi.org/project/adcircpy)) + - SCHISM (uses [PySCHISM](https://github.com/schism-dev/pyschism)) + - forcings + - ATMESH + - WW3DATA + - HURDAT best track + - OWI +- **platforms** + - local + - Slurm + - Hera + - Stampede2 + - Orion + +## organization / responsibility + +CoupledModelDriver is developed for the COASTAL Act project by the [Coastal Marine Modeling Branch (CMMB)](https://coastaloceanmodels.noaa.gov) of the Office of Coast Survey (OCS), a part of the [National Oceanic and Atmospheric Administration (NOAA)](https://www.noaa.gov), an agency of the United States federal government. + +- Zachary Burnett (**lead**) - zachary.burnett@noaa.gov +- William Pringle - wpringle@anl.gov +- Saeed Moghimi - saeed.moghimi@noaa.gov + +## usage example + +### 1. generate JSON configuration files + +`initialize_adcirc` creates JSON configuration files according to the given parameters. ADCIRC run options that are not exposed +by this command, such as `runs` or `gwce_solution_scheme`, can be specified by directly modifying the JSON files. The following +creates JSON files for coupling `(ATMESH + WW3DATA) -> ADCIRC` over a small Shinnecock Inlet mesh: + +```shell +initialize_adcirc \ + --platform HERA \ + --mesh-directory /scratch2/COASTAL/coastal/save/shared/models/meshes/shinnecock/v1.0 \ + --output-directory hera_shinnecock_ike_spinup_tidal_atmesh_ww3data \ + --modeled-start-time 20080823 \ + --modeled-duration 14:06:00:00 \ + --modeled-timestep 00:00:02 \ + --nems-interval 01:00:00 \ + --adcirc-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/NEMS-adcirc-atmesh-ww3data.x \ + --adcirc-processors 40 + --adcprep-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/adcprep \ + --modulefile /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/modulefiles/envmodules_intel.hera \ + --forcings tidal,atmesh,ww3data \ + --tidal-source TPXO \ + --tidal-path /scratch2/COASTAL/coastal/save/shared/models/forcings/tides/h_tpxo9.v1.nc \ + --tidal-spinup-duration 12:06:00:00 \ + --atmesh-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/wind_atm_fin_ch_time_vec.nc \ + --ww3data-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/ww3.Constant.20151214_sxy_ike_date.nc +``` + +This will create the directory `hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/` with the following JSON configuration files: + +``` +📂 hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ +┣ 📜 configure_adcirc.json +┣ 📜 configure_atmesh.json +┣ 📜 configure_modeldriver.json +┣ 📜 configure_nems.json +┣ 📜 configure_slurm.json +┣ 📜 configure_tidal_forcing.json +┗ 📜 configure_ww3data.json +``` + +These files contain relevant configuration values for an ADCIRC run. You will likely wish to change these values to alter the +resulting run, before generating the actual model configuration. For instance, NEMS connections and the run sequence need to be +manually specified in `configure_nems.json`. + +### 2. generate model configuration files + +`generate_adcirc` generates an ADCIRC run configuration (`fort.14`, `fort.15`, etc.) using options read from the JSON +configuration files (generated in the previous step). + +```shell +cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data +generate_adcirc +``` + +The resulting configuration will look like this: + +``` +📂 hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ +┣ 📜 configure_adcirc.json +┣ 📜 configure_atmesh.json +┣ 📜 configure_modeldriver.json +┣ 📜 configure_nems.json +┣ 📜 configure_slurm.json +┣ 📜 configure_tidal_forcing.json +┣ 📜 configure_ww3data.json +┣ 📂 spinup/ +┃ ┣ 📜 fort.13 +┃ ┣ 🔗 fort.14 -> ../fort.14 +┃ ┣ 📜 fort.15 +┃ ┣ 📜 nems.configure +┃ ┣ 📜 model_configure +┃ ┣ 🔗 atm_namelist.rc -> ./model_configure +┃ ┣ 📜 config.rc +┃ ┣ 📜 setup.job +┃ ┗ 📜 adcirc.job +┣ 📂 runs/ +┃ ┗ 📂 unperturbed/ +┃ ┣ 📜 fort.13 +┃ ┣ 🔗 fort.14 -> ../../fort.14 +┃ ┣ 📜 fort.15 +┃ ┣ 🔗 fort.67.nc -> ../../spinup/fort.67.nc +┃ ┣ 🔗 fort.68.nc -> ../../spinup/fort.68.nc +┃ ┣ 📜 nems.configure +┃ ┣ 📜 model_configure +┃ ┣ 🔗 atm_namelist.rc -> ./model_configure +┃ ┣ 📜 config.rc +┃ ┣ 📜 setup.job +┃ ┗ 📜 adcirc.job +┣ 📜 fort.14 +┣ 📜 cleanup.sh +┗ 📜 run_hera.sh +``` + +### 3. run the model + +The previous step will also have generated a script called `./run_hera.sh`. You can run it to submit the model run to the Slurm +job queue: + +```shell +./run_hera.sh +``` + +The queue will have the following jobs added: + +``` + JOBID CPU NODE DEPENDENCY NODELIST(REA NAME +20967647 1 1 (null) (None) ADCIRC_SETUP_SPINUP +20967648 40 1 afterok:20967647 (Dependency) ADCIRC_COLDSTART_SPINUP +20967649 1 1 (null) (None) ADCIRC_SETUP_unperturbed +20967650 42 2 afterok:20967649 (Dependency) ADCIRC_HOTSTART_unperturbed +``` + +### 4. track model progress + +`check_completion` checks the completion status of a running model directory. + +```shell +cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data +check_completion +``` + +```json +{ + "hera_shinnecock_ike_spinup_tidal_atmesh_ww3data": { + "spinup": "running - 15%", + "runs": "not_started - 0%" + } +} +``` + +you can also pass a specific directory (or several directories): + +```shell +check_completion spinup +``` + +```json +{ + "spinup": "running - 27%" +} +``` + +```shell +cd run_20211027_florence_besttrack_250msubset_quadrature +check_completion runs/*_13 +``` + +```json +{ + "vortex_4_variable_perturbation_13": "completed - 100.0%", + "vortex_4_variable_quadrature_13": "not_started - 0%" +} +``` + +if a run has an error, you can pass `--verbose` to see detailed logs: + +```shell +check_completion spinup +``` + +```json +{ + "spinup": "error - 0%" +} +``` + +```shell +check_completion spinup --verbose +``` + +```json +{ + "spinup": { + "status": "error", + "progress": "0%", + "error": { + "ADCIRC_SETUP_SPINUP.err.log": [ + "forrtl: severe (24): end-of-file during read, unit -4, file /proc/92195/fd/0\n", + "Image PC Routine Line Source \n", + "adcprep 000000000069A72E Unknown Unknown Unknown\n", + "adcprep 00000000006CBAAF Unknown Unknown Unknown\n", + "adcprep 000000000050A5CB openprepfiles_ 6996 prep.F\n", + "adcprep 0000000000507F22 prep13_ 753 prep.F\n", + "adcprep 000000000042E2E9 prepinput_ 717 adcprep.F\n", + "adcprep 000000000042BCDB MAIN__ 239 adcprep.F\n", + "adcprep 000000000040B65E Unknown Unknown Unknown\n", + "libc-2.17.so 00002AAEC02EB555 __libc_start_main Unknown Unknown\n", + "adcprep 000000000040B569 Unknown Unknown Unknown\n", + "srun: error: h24c51: task 0: Exited with exit code 24\n", + "srun: launch/slurm: _step_signal: Terminating StepId=25366266.1\n" + ] + } + } +} +``` + +```shell +check_completion runs +``` + +```json +{ + "spinup": "failed - 0%" +} +``` + +```shell +check_completion runs --verbose +``` + +```json +{ + "runs": { + "status": "failed", + "progress": "0%", + "failed": { + "fort.16": "ADCIRC output file `fort.16` not found" + }, + "error": { + "ADCIRC_SETUP_unperturbed.err.log": [ + "slurmstepd: error: execve(): /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ADCIRC/ALLBIN_INSTALL/adcprep: No such file or directory\n", + "srun: error: h18c49: task 0: Exited with exit code 2\n", + "srun: launch/slurm: _step_signal: Terminating StepId=25366268.0\n" + ] + } + } +} +``` + + +%package -n python3-coupledmodeldriver +Summary: coupled model configuration generation +Provides: python-coupledmodeldriver +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-coupledmodeldriver +# CoupledModelDriver + +[](https://github.com/noaa-ocs-modeling/CoupledModelDriver/actions?query=workflow%3Atests) +[](https://codecov.io/gh/noaa-ocs-modeling/coupledmodeldriver) +[](https://github.com/noaa-ocs-modeling/CoupledModelDriver/actions?query=workflow%3Abuild) +[](https://pypi.org/project/CoupledModelDriver) +[](https://creativecommons.org/share-your-work/public-domain/cc0) +[](https://sourceforge.net/p/oitnb/code) +[](https://coupledmodeldriver.readthedocs.io/en/latest/?badge=latest) + +CoupledModelDriver generates an overlying job submission framework and configuration directories for NEMS-coupled coastal ocean +model ensembles. + +```shell +pip install coupledmodeldriver +``` + +It utilizes [NEMSpy](https://nemspy.readthedocs.io) to generate NEMS configuration files, shares common configurations between +runs, and organizes spinup and mesh partition into separate jobs for dependant submission. + +Documentation can be found at https://coupledmodeldriver.readthedocs.io + +## supported models and platforms + +- **models** + - circulation models + - ADCIRC (uses [ADCIRCpy](https://pypi.org/project/adcircpy)) + - SCHISM (uses [PySCHISM](https://github.com/schism-dev/pyschism)) + - forcings + - ATMESH + - WW3DATA + - HURDAT best track + - OWI +- **platforms** + - local + - Slurm + - Hera + - Stampede2 + - Orion + +## organization / responsibility + +CoupledModelDriver is developed for the COASTAL Act project by the [Coastal Marine Modeling Branch (CMMB)](https://coastaloceanmodels.noaa.gov) of the Office of Coast Survey (OCS), a part of the [National Oceanic and Atmospheric Administration (NOAA)](https://www.noaa.gov), an agency of the United States federal government. + +- Zachary Burnett (**lead**) - zachary.burnett@noaa.gov +- William Pringle - wpringle@anl.gov +- Saeed Moghimi - saeed.moghimi@noaa.gov + +## usage example + +### 1. generate JSON configuration files + +`initialize_adcirc` creates JSON configuration files according to the given parameters. ADCIRC run options that are not exposed +by this command, such as `runs` or `gwce_solution_scheme`, can be specified by directly modifying the JSON files. The following +creates JSON files for coupling `(ATMESH + WW3DATA) -> ADCIRC` over a small Shinnecock Inlet mesh: + +```shell +initialize_adcirc \ + --platform HERA \ + --mesh-directory /scratch2/COASTAL/coastal/save/shared/models/meshes/shinnecock/v1.0 \ + --output-directory hera_shinnecock_ike_spinup_tidal_atmesh_ww3data \ + --modeled-start-time 20080823 \ + --modeled-duration 14:06:00:00 \ + --modeled-timestep 00:00:02 \ + --nems-interval 01:00:00 \ + --adcirc-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/NEMS-adcirc-atmesh-ww3data.x \ + --adcirc-processors 40 + --adcprep-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/adcprep \ + --modulefile /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/modulefiles/envmodules_intel.hera \ + --forcings tidal,atmesh,ww3data \ + --tidal-source TPXO \ + --tidal-path /scratch2/COASTAL/coastal/save/shared/models/forcings/tides/h_tpxo9.v1.nc \ + --tidal-spinup-duration 12:06:00:00 \ + --atmesh-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/wind_atm_fin_ch_time_vec.nc \ + --ww3data-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/ww3.Constant.20151214_sxy_ike_date.nc +``` + +This will create the directory `hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/` with the following JSON configuration files: + +``` +📂 hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ +┣ 📜 configure_adcirc.json +┣ 📜 configure_atmesh.json +┣ 📜 configure_modeldriver.json +┣ 📜 configure_nems.json +┣ 📜 configure_slurm.json +┣ 📜 configure_tidal_forcing.json +┗ 📜 configure_ww3data.json +``` + +These files contain relevant configuration values for an ADCIRC run. You will likely wish to change these values to alter the +resulting run, before generating the actual model configuration. For instance, NEMS connections and the run sequence need to be +manually specified in `configure_nems.json`. + +### 2. generate model configuration files + +`generate_adcirc` generates an ADCIRC run configuration (`fort.14`, `fort.15`, etc.) using options read from the JSON +configuration files (generated in the previous step). + +```shell +cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data +generate_adcirc +``` + +The resulting configuration will look like this: + +``` +📂 hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ +┣ 📜 configure_adcirc.json +┣ 📜 configure_atmesh.json +┣ 📜 configure_modeldriver.json +┣ 📜 configure_nems.json +┣ 📜 configure_slurm.json +┣ 📜 configure_tidal_forcing.json +┣ 📜 configure_ww3data.json +┣ 📂 spinup/ +┃ ┣ 📜 fort.13 +┃ ┣ 🔗 fort.14 -> ../fort.14 +┃ ┣ 📜 fort.15 +┃ ┣ 📜 nems.configure +┃ ┣ 📜 model_configure +┃ ┣ 🔗 atm_namelist.rc -> ./model_configure +┃ ┣ 📜 config.rc +┃ ┣ 📜 setup.job +┃ ┗ 📜 adcirc.job +┣ 📂 runs/ +┃ ┗ 📂 unperturbed/ +┃ ┣ 📜 fort.13 +┃ ┣ 🔗 fort.14 -> ../../fort.14 +┃ ┣ 📜 fort.15 +┃ ┣ 🔗 fort.67.nc -> ../../spinup/fort.67.nc +┃ ┣ 🔗 fort.68.nc -> ../../spinup/fort.68.nc +┃ ┣ 📜 nems.configure +┃ ┣ 📜 model_configure +┃ ┣ 🔗 atm_namelist.rc -> ./model_configure +┃ ┣ 📜 config.rc +┃ ┣ 📜 setup.job +┃ ┗ 📜 adcirc.job +┣ 📜 fort.14 +┣ 📜 cleanup.sh +┗ 📜 run_hera.sh +``` + +### 3. run the model + +The previous step will also have generated a script called `./run_hera.sh`. You can run it to submit the model run to the Slurm +job queue: + +```shell +./run_hera.sh +``` + +The queue will have the following jobs added: + +``` + JOBID CPU NODE DEPENDENCY NODELIST(REA NAME +20967647 1 1 (null) (None) ADCIRC_SETUP_SPINUP +20967648 40 1 afterok:20967647 (Dependency) ADCIRC_COLDSTART_SPINUP +20967649 1 1 (null) (None) ADCIRC_SETUP_unperturbed +20967650 42 2 afterok:20967649 (Dependency) ADCIRC_HOTSTART_unperturbed +``` + +### 4. track model progress + +`check_completion` checks the completion status of a running model directory. + +```shell +cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data +check_completion +``` + +```json +{ + "hera_shinnecock_ike_spinup_tidal_atmesh_ww3data": { + "spinup": "running - 15%", + "runs": "not_started - 0%" + } +} +``` + +you can also pass a specific directory (or several directories): + +```shell +check_completion spinup +``` + +```json +{ + "spinup": "running - 27%" +} +``` + +```shell +cd run_20211027_florence_besttrack_250msubset_quadrature +check_completion runs/*_13 +``` + +```json +{ + "vortex_4_variable_perturbation_13": "completed - 100.0%", + "vortex_4_variable_quadrature_13": "not_started - 0%" +} +``` + +if a run has an error, you can pass `--verbose` to see detailed logs: + +```shell +check_completion spinup +``` + +```json +{ + "spinup": "error - 0%" +} +``` + +```shell +check_completion spinup --verbose +``` + +```json +{ + "spinup": { + "status": "error", + "progress": "0%", + "error": { + "ADCIRC_SETUP_SPINUP.err.log": [ + "forrtl: severe (24): end-of-file during read, unit -4, file /proc/92195/fd/0\n", + "Image PC Routine Line Source \n", + "adcprep 000000000069A72E Unknown Unknown Unknown\n", + "adcprep 00000000006CBAAF Unknown Unknown Unknown\n", + "adcprep 000000000050A5CB openprepfiles_ 6996 prep.F\n", + "adcprep 0000000000507F22 prep13_ 753 prep.F\n", + "adcprep 000000000042E2E9 prepinput_ 717 adcprep.F\n", + "adcprep 000000000042BCDB MAIN__ 239 adcprep.F\n", + "adcprep 000000000040B65E Unknown Unknown Unknown\n", + "libc-2.17.so 00002AAEC02EB555 __libc_start_main Unknown Unknown\n", + "adcprep 000000000040B569 Unknown Unknown Unknown\n", + "srun: error: h24c51: task 0: Exited with exit code 24\n", + "srun: launch/slurm: _step_signal: Terminating StepId=25366266.1\n" + ] + } + } +} +``` + +```shell +check_completion runs +``` + +```json +{ + "spinup": "failed - 0%" +} +``` + +```shell +check_completion runs --verbose +``` + +```json +{ + "runs": { + "status": "failed", + "progress": "0%", + "failed": { + "fort.16": "ADCIRC output file `fort.16` not found" + }, + "error": { + "ADCIRC_SETUP_unperturbed.err.log": [ + "slurmstepd: error: execve(): /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ADCIRC/ALLBIN_INSTALL/adcprep: No such file or directory\n", + "srun: error: h18c49: task 0: Exited with exit code 2\n", + "srun: launch/slurm: _step_signal: Terminating StepId=25366268.0\n" + ] + } + } +} +``` + + +%package help +Summary: Development documents and examples for coupledmodeldriver +Provides: python3-coupledmodeldriver-doc +%description help +# CoupledModelDriver + +[](https://github.com/noaa-ocs-modeling/CoupledModelDriver/actions?query=workflow%3Atests) +[](https://codecov.io/gh/noaa-ocs-modeling/coupledmodeldriver) +[](https://github.com/noaa-ocs-modeling/CoupledModelDriver/actions?query=workflow%3Abuild) +[](https://pypi.org/project/CoupledModelDriver) +[](https://creativecommons.org/share-your-work/public-domain/cc0) +[](https://sourceforge.net/p/oitnb/code) +[](https://coupledmodeldriver.readthedocs.io/en/latest/?badge=latest) + +CoupledModelDriver generates an overlying job submission framework and configuration directories for NEMS-coupled coastal ocean +model ensembles. + +```shell +pip install coupledmodeldriver +``` + +It utilizes [NEMSpy](https://nemspy.readthedocs.io) to generate NEMS configuration files, shares common configurations between +runs, and organizes spinup and mesh partition into separate jobs for dependant submission. + +Documentation can be found at https://coupledmodeldriver.readthedocs.io + +## supported models and platforms + +- **models** + - circulation models + - ADCIRC (uses [ADCIRCpy](https://pypi.org/project/adcircpy)) + - SCHISM (uses [PySCHISM](https://github.com/schism-dev/pyschism)) + - forcings + - ATMESH + - WW3DATA + - HURDAT best track + - OWI +- **platforms** + - local + - Slurm + - Hera + - Stampede2 + - Orion + +## organization / responsibility + +CoupledModelDriver is developed for the COASTAL Act project by the [Coastal Marine Modeling Branch (CMMB)](https://coastaloceanmodels.noaa.gov) of the Office of Coast Survey (OCS), a part of the [National Oceanic and Atmospheric Administration (NOAA)](https://www.noaa.gov), an agency of the United States federal government. + +- Zachary Burnett (**lead**) - zachary.burnett@noaa.gov +- William Pringle - wpringle@anl.gov +- Saeed Moghimi - saeed.moghimi@noaa.gov + +## usage example + +### 1. generate JSON configuration files + +`initialize_adcirc` creates JSON configuration files according to the given parameters. ADCIRC run options that are not exposed +by this command, such as `runs` or `gwce_solution_scheme`, can be specified by directly modifying the JSON files. The following +creates JSON files for coupling `(ATMESH + WW3DATA) -> ADCIRC` over a small Shinnecock Inlet mesh: + +```shell +initialize_adcirc \ + --platform HERA \ + --mesh-directory /scratch2/COASTAL/coastal/save/shared/models/meshes/shinnecock/v1.0 \ + --output-directory hera_shinnecock_ike_spinup_tidal_atmesh_ww3data \ + --modeled-start-time 20080823 \ + --modeled-duration 14:06:00:00 \ + --modeled-timestep 00:00:02 \ + --nems-interval 01:00:00 \ + --adcirc-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/NEMS-adcirc-atmesh-ww3data.x \ + --adcirc-processors 40 + --adcprep-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/adcprep \ + --modulefile /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/modulefiles/envmodules_intel.hera \ + --forcings tidal,atmesh,ww3data \ + --tidal-source TPXO \ + --tidal-path /scratch2/COASTAL/coastal/save/shared/models/forcings/tides/h_tpxo9.v1.nc \ + --tidal-spinup-duration 12:06:00:00 \ + --atmesh-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/wind_atm_fin_ch_time_vec.nc \ + --ww3data-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/ww3.Constant.20151214_sxy_ike_date.nc +``` + +This will create the directory `hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/` with the following JSON configuration files: + +``` +📂 hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ +┣ 📜 configure_adcirc.json +┣ 📜 configure_atmesh.json +┣ 📜 configure_modeldriver.json +┣ 📜 configure_nems.json +┣ 📜 configure_slurm.json +┣ 📜 configure_tidal_forcing.json +┗ 📜 configure_ww3data.json +``` + +These files contain relevant configuration values for an ADCIRC run. You will likely wish to change these values to alter the +resulting run, before generating the actual model configuration. For instance, NEMS connections and the run sequence need to be +manually specified in `configure_nems.json`. + +### 2. generate model configuration files + +`generate_adcirc` generates an ADCIRC run configuration (`fort.14`, `fort.15`, etc.) using options read from the JSON +configuration files (generated in the previous step). + +```shell +cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data +generate_adcirc +``` + +The resulting configuration will look like this: + +``` +📂 hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ +┣ 📜 configure_adcirc.json +┣ 📜 configure_atmesh.json +┣ 📜 configure_modeldriver.json +┣ 📜 configure_nems.json +┣ 📜 configure_slurm.json +┣ 📜 configure_tidal_forcing.json +┣ 📜 configure_ww3data.json +┣ 📂 spinup/ +┃ ┣ 📜 fort.13 +┃ ┣ 🔗 fort.14 -> ../fort.14 +┃ ┣ 📜 fort.15 +┃ ┣ 📜 nems.configure +┃ ┣ 📜 model_configure +┃ ┣ 🔗 atm_namelist.rc -> ./model_configure +┃ ┣ 📜 config.rc +┃ ┣ 📜 setup.job +┃ ┗ 📜 adcirc.job +┣ 📂 runs/ +┃ ┗ 📂 unperturbed/ +┃ ┣ 📜 fort.13 +┃ ┣ 🔗 fort.14 -> ../../fort.14 +┃ ┣ 📜 fort.15 +┃ ┣ 🔗 fort.67.nc -> ../../spinup/fort.67.nc +┃ ┣ 🔗 fort.68.nc -> ../../spinup/fort.68.nc +┃ ┣ 📜 nems.configure +┃ ┣ 📜 model_configure +┃ ┣ 🔗 atm_namelist.rc -> ./model_configure +┃ ┣ 📜 config.rc +┃ ┣ 📜 setup.job +┃ ┗ 📜 adcirc.job +┣ 📜 fort.14 +┣ 📜 cleanup.sh +┗ 📜 run_hera.sh +``` + +### 3. run the model + +The previous step will also have generated a script called `./run_hera.sh`. You can run it to submit the model run to the Slurm +job queue: + +```shell +./run_hera.sh +``` + +The queue will have the following jobs added: + +``` + JOBID CPU NODE DEPENDENCY NODELIST(REA NAME +20967647 1 1 (null) (None) ADCIRC_SETUP_SPINUP +20967648 40 1 afterok:20967647 (Dependency) ADCIRC_COLDSTART_SPINUP +20967649 1 1 (null) (None) ADCIRC_SETUP_unperturbed +20967650 42 2 afterok:20967649 (Dependency) ADCIRC_HOTSTART_unperturbed +``` + +### 4. track model progress + +`check_completion` checks the completion status of a running model directory. + +```shell +cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data +check_completion +``` + +```json +{ + "hera_shinnecock_ike_spinup_tidal_atmesh_ww3data": { + "spinup": "running - 15%", + "runs": "not_started - 0%" + } +} +``` + +you can also pass a specific directory (or several directories): + +```shell +check_completion spinup +``` + +```json +{ + "spinup": "running - 27%" +} +``` + +```shell +cd run_20211027_florence_besttrack_250msubset_quadrature +check_completion runs/*_13 +``` + +```json +{ + "vortex_4_variable_perturbation_13": "completed - 100.0%", + "vortex_4_variable_quadrature_13": "not_started - 0%" +} +``` + +if a run has an error, you can pass `--verbose` to see detailed logs: + +```shell +check_completion spinup +``` + +```json +{ + "spinup": "error - 0%" +} +``` + +```shell +check_completion spinup --verbose +``` + +```json +{ + "spinup": { + "status": "error", + "progress": "0%", + "error": { + "ADCIRC_SETUP_SPINUP.err.log": [ + "forrtl: severe (24): end-of-file during read, unit -4, file /proc/92195/fd/0\n", + "Image PC Routine Line Source \n", + "adcprep 000000000069A72E Unknown Unknown Unknown\n", + "adcprep 00000000006CBAAF Unknown Unknown Unknown\n", + "adcprep 000000000050A5CB openprepfiles_ 6996 prep.F\n", + "adcprep 0000000000507F22 prep13_ 753 prep.F\n", + "adcprep 000000000042E2E9 prepinput_ 717 adcprep.F\n", + "adcprep 000000000042BCDB MAIN__ 239 adcprep.F\n", + "adcprep 000000000040B65E Unknown Unknown Unknown\n", + "libc-2.17.so 00002AAEC02EB555 __libc_start_main Unknown Unknown\n", + "adcprep 000000000040B569 Unknown Unknown Unknown\n", + "srun: error: h24c51: task 0: Exited with exit code 24\n", + "srun: launch/slurm: _step_signal: Terminating StepId=25366266.1\n" + ] + } + } +} +``` + +```shell +check_completion runs +``` + +```json +{ + "spinup": "failed - 0%" +} +``` + +```shell +check_completion runs --verbose +``` + +```json +{ + "runs": { + "status": "failed", + "progress": "0%", + "failed": { + "fort.16": "ADCIRC output file `fort.16` not found" + }, + "error": { + "ADCIRC_SETUP_unperturbed.err.log": [ + "slurmstepd: error: execve(): /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ADCIRC/ALLBIN_INSTALL/adcprep: No such file or directory\n", + "srun: error: h18c49: task 0: Exited with exit code 2\n", + "srun: launch/slurm: _step_signal: Terminating StepId=25366268.0\n" + ] + } + } +} +``` + + +%prep +%autosetup -n coupledmodeldriver-1.6.5 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-coupledmodeldriver -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 1.6.5-1 +- Package Spec generated @@ -0,0 +1 @@ +513e382f938cf6a6802b5015b14f69af coupledmodeldriver-1.6.5.tar.gz |